Enhancing the pharmaceutical properties of protein drugs by ancestral sequence reconstruction

Abstract

Optimization of a protein's pharmaceutical properties is usually carried out by rational design and/or directed evolution. Here we test an alternative approach based on ancestral sequence reconstruction. Using available genomic sequence data on coagulation factor VIII and predictive models of molecular evolution, we engineer protein variants with improved activity, stability, and biosynthesis potential and reduced inhibition by anti-drug antibodies. In principle, this approach can be applied to any protein drug based on a conserved gene sequence.

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Figure 1: An-FVIII phylogeny, recombinant productivity and cofactor stability analysis.
Figure 2: An-FVIII immune safety and in vivo pharmacology studies.

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Acknowledgements

This work was supported by funding from the National Institutes of Health/National Heart, Lung, and Blood Institute for the Translational Research Centers in Thrombotic and Hemostatic Disorders (U54 HL112309 to H.T.S., S.L.M., and C.B.D.), the Bayer Hemophilia Awards Program, Bayer HealthCare (C.B.D.) as well as a research partnership between Children's Healthcare of Atlanta and the Georgia Institute of Technology (C.B.D. and E.A.G.). We also thank E.T. Parker (Aflac Cancer and Blood Disorders Center, Department of Pediatrics, Emory University, Atlanta, Georgia, USA) for technical assistance with the in vivo mouse studies.

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Contributions

P.M.Z. designed and performed experiments, analyzed the data, and drafted the manuscript. H.C.B. performed gene transfer experiments and edited the manuscript. K.K. performed experiments. S.L.M. contributed reagents, designed experiments, analyzed data and edited the manuscript. H.T.S. conceived the project, designed experiments, analyzed data and edited the manuscript. E.A.G. performed ASR and edited the manuscript. C.B.D. conceived the project, designed experiments, analyzed data and drafted and edited the manuscript.

Corresponding author

Correspondence to Christopher B Doering.

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Competing interests

C.B.D., E.A.G., H.T.S. and P.M.Z. are inventors on a patent application describing ancestral FVIII technology filed by Emory University/Children's Healthcare of Atlanta and the Georgia Institute of Technology. C.B.D. and H.T.S. are co-founders of Expression Therapeutics, LLC, and own equity in the company. Expression Therapeutics owns the intellectual property associated with ET3 and has plans to commercially develop technology used in the research described in this paper. The terms of this arrangement have been reviewed and approved by Emory University in accordance with its conflict of interest policies.

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Supplementary Figures 1–12, Supplementary Tables 1–3 and Supplementary Note (PDF 2791 kb)

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Zakas, P., Brown, H., Knight, K. et al. Enhancing the pharmaceutical properties of protein drugs by ancestral sequence reconstruction. Nat Biotechnol 35, 35–37 (2017). https://doi.org/10.1038/nbt.3677

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